data_1KSJ # _model_server_result.job_id PGhJeaWpEbBVP7GXlQV1Iw _model_server_result.datetime_utc '2024-11-05 13:45:01' _model_server_result.server_version 0.9.12 _model_server_result.query_name ligand _model_server_result.source_id pdb-bcif _model_server_result.entry_id 1ksj # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"F","auth_seq_id":201}' # _entry.id 1KSJ # _exptl.entry_id 1KSJ _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 443.201 _entity.id 6 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "GUANOSINE-5'-DIPHOSPHATE" _entity.pdbx_number_of_molecules 1 _entity.pdbx_parent_entity_id . _entity.pdbx_mutation ? _entity.pdbx_fragment ? _entity.pdbx_ec ? # _cell.angle_alpha 90 _cell.angle_beta 90 _cell.angle_gamma 90 _cell.entry_id 1KSJ _cell.length_a 44.815 _cell.length_b 65.726 _cell.length_c 103.99 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 1KSJ _symmetry.cell_setting orthorhombic _symmetry.Int_Tables_number 19 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 21 21 21' # _pdbx_struct_assembly.method_details ? _pdbx_struct_assembly.oligomeric_details dimeric _pdbx_struct_assembly.oligomeric_count 2 _pdbx_struct_assembly.details author_defined_assembly _pdbx_struct_assembly.id 1 # _pdbx_struct_assembly_gen.asym_id_list A,B,C,D,E,F,G,H,I _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 1 # _pdbx_struct_oper_list.id 1 _pdbx_struct_oper_list.type 'identity operation' _pdbx_struct_oper_list.name 1_555 _pdbx_struct_oper_list.symmetry_operation x,y,z _pdbx_struct_oper_list.matrix[1][1] 1 _pdbx_struct_oper_list.matrix[1][2] 0 _pdbx_struct_oper_list.matrix[1][3] 0 _pdbx_struct_oper_list.matrix[2][1] 0 _pdbx_struct_oper_list.matrix[2][2] 1 _pdbx_struct_oper_list.matrix[2][3] 0 _pdbx_struct_oper_list.matrix[3][1] 0 _pdbx_struct_oper_list.matrix[3][2] 0 _pdbx_struct_oper_list.matrix[3][3] 1 _pdbx_struct_oper_list.vector[1] 0 _pdbx_struct_oper_list.vector[2] 0 _pdbx_struct_oper_list.vector[3] 0 # _struct_asym.details ? _struct_asym.entity_id 6 _struct_asym.id F _struct_asym.pdbx_modified N _struct_asym.pdbx_blank_PDB_chainid_flag N # loop_ _struct_conn.conn_type_id _struct_conn.details _struct_conn.id _struct_conn.ptnr1_label_asym_id _struct_conn.ptnr1_label_atom_id _struct_conn.ptnr1_label_comp_id _struct_conn.ptnr1_label_seq_id _struct_conn.ptnr1_auth_asym_id _struct_conn.ptnr1_auth_comp_id _struct_conn.ptnr1_auth_seq_id _struct_conn.ptnr1_symmetry _struct_conn.ptnr2_label_asym_id _struct_conn.ptnr2_label_atom_id _struct_conn.ptnr2_label_comp_id _struct_conn.ptnr2_label_seq_id _struct_conn.ptnr2_auth_asym_id _struct_conn.ptnr2_auth_comp_id _struct_conn.ptnr2_auth_seq_id _struct_conn.ptnr2_symmetry _struct_conn.pdbx_ptnr1_PDB_ins_code _struct_conn.pdbx_ptnr1_label_alt_id _struct_conn.pdbx_ptnr1_standard_comp_id _struct_conn.pdbx_ptnr2_PDB_ins_code _struct_conn.pdbx_ptnr2_label_alt_id _struct_conn.pdbx_ptnr3_PDB_ins_code _struct_conn.pdbx_ptnr3_label_alt_id _struct_conn.pdbx_ptnr3_label_asym_id _struct_conn.pdbx_ptnr3_label_atom_id _struct_conn.pdbx_ptnr3_label_comp_id _struct_conn.pdbx_ptnr3_label_seq_id _struct_conn.pdbx_PDB_id _struct_conn.pdbx_dist_value _struct_conn.pdbx_value_order covale ? covale1 A C LEU 22 A LEU 20 1_555 A N MSE 23 A MSE 21 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.332 ? covale ? covale2 A C MSE 23 A MSE 21 1_555 A N LEU 24 A LEU 22 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.332 ? covale ? covale3 A C ARG 100 A ARG 98 1_555 A N MSE 101 A MSE 99 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.324 ? covale ? covale4 A C MSE 101 A MSE 99 1_555 A N GLN 102 A GLN 100 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.331 ? covale ? covale5 A C SER 136 A SER 134 1_555 A N CME 137 A CME 135 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.33 ? covale ? covale6 A C CME 137 A CME 135 1_555 A N ASN 138 A ASN 136 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.327 ? covale ? covale7 B C TRP 21 B TRP 19 1_555 B N MSE 22 B MSE 20 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.325 ? covale ? covale8 B C MSE 22 B MSE 20 1_555 B N ASN 23 B ASN 21 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.333 ? covale ? covale9 B C GLN 72 B GLN 70 1_555 B N MSE 73 B MSE 71 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.332 ? covale ? covale10 B C MSE 73 B MSE 71 1_555 B N GLU 74 B GLU 72 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.328 ? covale ? covale11 B C GLN 87 B GLN 85 1_555 B N CME 88 B CME 86 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.329 ? covale ? covale12 B C CME 88 B CME 86 1_555 B N LEU 89 B LEU 87 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.33 ? metalc ? metalc1 A OG1 THR 32 A THR 30 1_555 D MG MG . A MG 205 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.031 ? metalc ? metalc2 A OG1 THR 49 A THR 47 1_555 D MG MG . A MG 205 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.018 ? metalc ? metalc3 F O1B GDP . A GDP 201 1_555 D MG MG . A MG 205 1_555 ? A ? ? ? ? ? ? ? ? ? ? 2.291 ? metalc ? metalc4 C O1 PO4 . A PO4 202 1_555 D MG MG . A MG 205 1_555 ? A ? ? ? ? ? ? ? ? ? ? 1.816 ? metalc ? metalc5 G O2B GTP . A GTP 203 1_555 D MG MG . A MG 205 1_555 ? B ? ? ? ? ? ? ? ? ? ? 2.135 ? metalc ? metalc6 G O2G GTP . A GTP 203 1_555 D MG MG . A MG 205 1_555 ? B ? ? ? ? ? ? ? ? ? ? 2.089 ? metalc ? metalc7 D MG MG . A MG 205 1_555 H O HOH . A HOH 239 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.162 ? metalc ? metalc8 D MG MG . A MG 205 1_555 H O HOH . A HOH 240 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.175 ? # _chem_comp.formula 'C10 H15 N5 O11 P2' _chem_comp.formula_weight 443.201 _chem_comp.id GDP _chem_comp.mon_nstd_flag n _chem_comp.name "GUANOSINE-5'-DIPHOSPHATE" _chem_comp.type 'rna linking' _chem_comp.pdbx_synonyms ? # loop_ _chem_comp_bond.atom_id_1 _chem_comp_bond.atom_id_2 _chem_comp_bond.comp_id _chem_comp_bond.value_order _chem_comp_bond.pdbx_ordinal _chem_comp_bond.pdbx_stereo_config _chem_comp_bond.pdbx_aromatic_flag PB O1B GDP doub 113 n n PB O2B GDP sing 114 n n PB O3B GDP sing 115 n n PB O3A GDP sing 116 n n O2B HOB2 GDP sing 117 n n O3B HOB3 GDP sing 118 n n O3A PA GDP sing 119 n n PA O1A GDP doub 120 n n PA O2A GDP sing 121 n n PA O5' GDP sing 122 n n O2A HOA2 GDP sing 123 n n O5' C5' GDP sing 124 n n C5' C4' GDP sing 125 n n C5' H5' GDP sing 126 n n C5' "H5''" GDP sing 127 n n C4' O4' GDP sing 128 n n C4' C3' GDP sing 129 n n C4' H4' GDP sing 130 n n O4' C1' GDP sing 131 n n C3' O3' GDP sing 132 n n C3' C2' GDP sing 133 n n C3' H3' GDP sing 134 n n O3' HO3' GDP sing 135 n n C2' O2' GDP sing 136 n n C2' C1' GDP sing 137 n n C2' H2' GDP sing 138 n n O2' HO2' GDP sing 139 n n C1' N9 GDP sing 140 n n C1' H1' GDP sing 141 n n N9 C8 GDP sing 142 n y N9 C4 GDP sing 143 n y C8 N7 GDP doub 144 n y C8 H8 GDP sing 145 n n N7 C5 GDP sing 146 n y C5 C6 GDP sing 147 n n C5 C4 GDP doub 148 n y C6 O6 GDP doub 149 n n C6 N1 GDP sing 150 n n N1 C2 GDP sing 151 n n N1 HN1 GDP sing 152 n n C2 N2 GDP sing 153 n n C2 N3 GDP doub 154 n n N2 HN21 GDP sing 155 n n N2 HN22 GDP sing 156 n n N3 C4 GDP sing 157 n n # _atom_sites.entry_id 1KSJ _atom_sites.fract_transf_matrix[1][1] 0.022314 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.015215 _atom_sites.fract_transf_matrix[2][3] 0 _atom_sites.fract_transf_matrix[3][1] 0 _atom_sites.fract_transf_matrix[3][2] 0 _atom_sites.fract_transf_matrix[3][3] 0.009616 _atom_sites.fract_transf_vector[1] 0 _atom_sites.fract_transf_vector[2] 0 _atom_sites.fract_transf_vector[3] 0 # loop_ _pdbx_nonpoly_scheme.asym_id _pdbx_nonpoly_scheme.entity_id _pdbx_nonpoly_scheme.mon_id _pdbx_nonpoly_scheme.pdb_strand_id _pdbx_nonpoly_scheme.ndb_seq_num _pdbx_nonpoly_scheme.pdb_seq_num _pdbx_nonpoly_scheme.auth_seq_num _pdbx_nonpoly_scheme.pdb_mon_id _pdbx_nonpoly_scheme.auth_mon_id _pdbx_nonpoly_scheme.pdb_ins_code C 3 PO4 A 1 202 202 PO4 PO4 . D 4 MG A 1 205 205 MG MG . E 5 BME A 1 236 236 BME BME . F 6 GDP A 1 201 201 GDP GDP . G 7 GTP A 1 203 203 GTP GTP . H 8 HOH A 1 237 204 HOH HOH . H 8 HOH A 2 238 1 HOH HOH . H 8 HOH A 3 239 2 HOH HOH . H 8 HOH A 4 240 3 HOH HOH . H 8 HOH A 5 241 7 HOH HOH . H 8 HOH A 6 242 10 HOH HOH . H 8 HOH A 7 243 11 HOH HOH . H 8 HOH A 8 244 12 HOH HOH . H 8 HOH A 9 245 13 HOH HOH . H 8 HOH A 10 246 18 HOH HOH . H 8 HOH A 11 247 19 HOH HOH . H 8 HOH A 12 248 21 HOH HOH . H 8 HOH A 13 249 22 HOH HOH . H 8 HOH A 14 250 23 HOH HOH . H 8 HOH A 15 251 24 HOH HOH . H 8 HOH A 16 252 25 HOH HOH . H 8 HOH A 17 253 27 HOH HOH . H 8 HOH A 18 254 29 HOH HOH . H 8 HOH A 19 255 31 HOH HOH . H 8 HOH A 20 256 33 HOH HOH . H 8 HOH A 21 257 35 HOH HOH . H 8 HOH A 22 258 36 HOH HOH . H 8 HOH A 23 259 39 HOH HOH . H 8 HOH A 24 260 40 HOH HOH . H 8 HOH A 25 261 42 HOH HOH . H 8 HOH A 26 262 43 HOH HOH . H 8 HOH A 27 263 44 HOH HOH . H 8 HOH A 28 264 45 HOH HOH . H 8 HOH A 29 265 47 HOH HOH . H 8 HOH A 30 266 52 HOH HOH . H 8 HOH A 31 267 58 HOH HOH . H 8 HOH A 32 268 59 HOH HOH . H 8 HOH A 33 269 62 HOH HOH . H 8 HOH A 34 270 67 HOH HOH . H 8 HOH A 35 271 68 HOH HOH . H 8 HOH A 36 272 69 HOH HOH . H 8 HOH A 37 273 70 HOH HOH . H 8 HOH A 38 274 74 HOH HOH . H 8 HOH A 39 275 75 HOH HOH . H 8 HOH A 40 276 77 HOH HOH . H 8 HOH A 41 277 78 HOH HOH . H 8 HOH A 42 278 81 HOH HOH . H 8 HOH A 43 279 84 HOH HOH . H 8 HOH A 44 280 87 HOH HOH . H 8 HOH A 45 281 90 HOH HOH . H 8 HOH A 46 282 92 HOH HOH . H 8 HOH A 47 283 93 HOH HOH . H 8 HOH A 48 284 100 HOH HOH . H 8 HOH A 49 285 103 HOH HOH . H 8 HOH A 50 286 104 HOH HOH . H 8 HOH A 51 287 116 HOH HOH . H 8 HOH A 52 288 118 HOH HOH . H 8 HOH A 53 289 119 HOH HOH . H 8 HOH A 54 290 125 HOH HOH . H 8 HOH A 55 291 129 HOH HOH . H 8 HOH A 56 292 130 HOH HOH . H 8 HOH A 57 293 133 HOH HOH . I 8 HOH B 1 151 4 HOH HOH . I 8 HOH B 2 152 5 HOH HOH . I 8 HOH B 3 153 6 HOH HOH . I 8 HOH B 4 154 8 HOH HOH . I 8 HOH B 5 155 9 HOH HOH . I 8 HOH B 6 156 14 HOH HOH . I 8 HOH B 7 157 15 HOH HOH . I 8 HOH B 8 158 16 HOH HOH . I 8 HOH B 9 159 17 HOH HOH . I 8 HOH B 10 160 28 HOH HOH . I 8 HOH B 11 161 32 HOH HOH . I 8 HOH B 12 162 34 HOH HOH . I 8 HOH B 13 163 37 HOH HOH . I 8 HOH B 14 164 38 HOH HOH . I 8 HOH B 15 165 41 HOH HOH . I 8 HOH B 16 166 48 HOH HOH . I 8 HOH B 17 167 49 HOH HOH . I 8 HOH B 18 168 50 HOH HOH . I 8 HOH B 19 169 51 HOH HOH . I 8 HOH B 20 170 53 HOH HOH . I 8 HOH B 21 171 56 HOH HOH . I 8 HOH B 22 172 57 HOH HOH . I 8 HOH B 23 173 71 HOH HOH . I 8 HOH B 24 174 72 HOH HOH . I 8 HOH B 25 175 73 HOH HOH . I 8 HOH B 26 176 80 HOH HOH . I 8 HOH B 27 177 82 HOH HOH . I 8 HOH B 28 178 83 HOH HOH . I 8 HOH B 29 179 85 HOH HOH . I 8 HOH B 30 180 86 HOH HOH . I 8 HOH B 31 181 88 HOH HOH . I 8 HOH B 32 182 89 HOH HOH . I 8 HOH B 33 183 91 HOH HOH . I 8 HOH B 34 184 94 HOH HOH . I 8 HOH B 35 185 95 HOH HOH . I 8 HOH B 36 186 96 HOH HOH . I 8 HOH B 37 187 98 HOH HOH . I 8 HOH B 38 188 99 HOH HOH . I 8 HOH B 39 189 101 HOH HOH . I 8 HOH B 40 190 105 HOH HOH . I 8 HOH B 41 191 107 HOH HOH . I 8 HOH B 42 192 110 HOH HOH . I 8 HOH B 43 193 115 HOH HOH . I 8 HOH B 44 194 120 HOH HOH . I 8 HOH B 45 195 122 HOH HOH . I 8 HOH B 46 196 127 HOH HOH . I 8 HOH B 47 197 128 HOH HOH . I 8 HOH B 48 198 131 HOH HOH . # loop_ _atom_site.group_PDB _atom_site.id _atom_site.type_symbol _atom_site.label_atom_id _atom_site.label_comp_id _atom_site.label_seq_id _atom_site.label_alt_id _atom_site.pdbx_PDB_ins_code _atom_site.label_asym_id _atom_site.label_entity_id _atom_site.Cartn_x _atom_site.Cartn_y _atom_site.Cartn_z _atom_site.occupancy _atom_site.B_iso_or_equiv _atom_site.pdbx_formal_charge _atom_site.auth_atom_id _atom_site.auth_comp_id _atom_site.auth_seq_id _atom_site.auth_asym_id _atom_site.pdbx_PDB_model_num HETATM 1 P PB GDP . A . F 6 14.882 4.05 39.587 0.74 41.28 ? PB GDP 201 A 1 HETATM 2 O O1B GDP . A . F 6 16.361 4.175 39.997 0.74 45.86 ? O1B GDP 201 A 1 HETATM 3 O O2B GDP . A . F 6 14.202 5.222 39.049 0.74 46.52 ? O2B GDP 201 A 1 HETATM 4 O O3B GDP . A . F 6 14.762 2.849 38.468 0.74 41.5 ? O3B GDP 201 A 1 HETATM 5 O O3A GDP . A . F 6 14.053 3.486 40.783 0.74 40.09 ? O3A GDP 201 A 1 HETATM 6 P PA GDP . A . F 6 14.357 2.272 41.787 0.74 38.46 ? PA GDP 201 A 1 HETATM 7 O O1A GDP . A . F 6 15.166 1.238 41.171 0.74 43.25 ? O1A GDP 201 A 1 HETATM 8 O O2A GDP . A . F 6 14.847 2.928 43.086 0.74 43.31 ? O2A GDP 201 A 1 HETATM 9 O O5' GDP . A . F 6 12.838 1.59 41.97 0.74 38.82 ? O5' GDP 201 A 1 HETATM 10 C C5' GDP . A . F 6 11.854 2.505 42.616 0.74 38.03 ? C5' GDP 201 A 1 HETATM 11 C C4' GDP . A . F 6 11.055 1.394 43.479 0.74 38.24 ? C4' GDP 201 A 1 HETATM 12 O O4' GDP . A . F 6 10.437 0.305 42.756 0.74 38.4 ? O4' GDP 201 A 1 HETATM 13 C C3' GDP . A . F 6 11.684 0.775 44.61 0.74 38.72 ? C3' GDP 201 A 1 HETATM 14 O O3' GDP . A . F 6 10.875 0.838 45.757 0.74 40.22 ? O3' GDP 201 A 1 HETATM 15 C C2' GDP . A . F 6 12.139 -0.674 44.25 0.74 38.4 ? C2' GDP 201 A 1 HETATM 16 O O2' GDP . A . F 6 12.073 -1.486 45.281 0.74 38.64 ? O2' GDP 201 A 1 HETATM 17 C C1' GDP . A . F 6 10.696 -0.971 43.373 0.74 37.52 ? C1' GDP 201 A 1 HETATM 18 N N9 GDP . A . F 6 11.02 -1.931 42.241 0.74 36.27 ? N9 GDP 201 A 1 HETATM 19 C C8 GDP . A . F 6 12.107 -1.765 41.384 0.74 35.31 ? C8 GDP 201 A 1 HETATM 20 N N7 GDP . A . F 6 11.88 -2.829 40.581 0.74 34.78 ? N7 GDP 201 A 1 HETATM 21 C C5 GDP . A . F 6 10.749 -3.604 40.884 0.74 34.8 ? C5 GDP 201 A 1 HETATM 22 C C6 GDP . A . F 6 10.297 -4.615 40.268 0.74 33.99 ? C6 GDP 201 A 1 HETATM 23 O O6 GDP . A . F 6 10.534 -5.325 39.245 0.74 32.92 ? O6 GDP 201 A 1 HETATM 24 N N1 GDP . A . F 6 9.05 -5.119 40.932 0.74 34.16 ? N1 GDP 201 A 1 HETATM 25 C C2 GDP . A . F 6 8.684 -4.466 41.963 0.74 33.8 ? C2 GDP 201 A 1 HETATM 26 N N2 GDP . A . F 6 7.426 -4.989 42.583 0.74 32.71 ? N2 GDP 201 A 1 HETATM 27 N N3 GDP . A . F 6 9.148 -3.4 42.607 0.74 35.06 ? N3 GDP 201 A 1 HETATM 28 C C4 GDP . A . F 6 10.244 -3.021 41.944 0.74 35.45 ? C4 GDP 201 A 1 # _model_server_stats.io_time_ms 11 _model_server_stats.parse_time_ms 20 _model_server_stats.create_model_time_ms 8 _model_server_stats.query_time_ms 325 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 28 #